Variant report

Variant	rs9450661
Chromosome Location	chr6:88081647-88081648
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:88074461..88076476-chr6:88079335..88082182,2	K562	blood:
2	chr6:88074976..88076757-chr6:88079576..88082182,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10944310	0.80[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs11962148	0.91[CHB][hapmap]
rs11965562	0.91[CHB][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap]
rs11970696	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs12524205	0.82[CHB][hapmap]
rs12525533	0.86[AMR][1000 genomes]
rs13214442	0.90[CHB][hapmap]
rs1328477	0.81[CHB][hapmap];0.87[MEX][hapmap]
rs16879240	0.89[ASN][1000 genomes]
rs16879887	0.86[CHB][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes]
rs16879893	0.91[CHB][hapmap]
rs2092648	0.83[AMR][1000 genomes]
rs2092850	0.90[ASN][1000 genomes]
rs2180177	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2223877	0.91[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap]
rs2246051	0.91[CHB][hapmap]
rs2246057	0.91[CHB][hapmap]
rs2268996	0.91[CHB][hapmap]
rs2295088	0.87[GIH][hapmap];0.94[JPT][hapmap]
rs2300898	0.82[CHB][hapmap]
rs2300899	0.91[CHB][hapmap]
rs2300900	0.82[CHB][hapmap]
rs2300904	0.89[CHB][hapmap]
rs2300908	0.91[CHB][hapmap]
rs2875533	0.95[MEX][hapmap]
rs3778671	0.91[CHB][hapmap]
rs3818057	0.82[CHB][hapmap]
rs4707364	0.92[ASN][1000 genomes]
rs58306197	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6915077	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs6927171	0.90[CHB][hapmap]
rs6928057	0.91[CHB][hapmap]
rs728582	0.91[CHB][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes]
rs73490158	0.91[ASN][1000 genomes]
rs7649	0.82[CHB][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap]
rs7761943	0.91[CHB][hapmap]
rs9444499	0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes]
rs9444501	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs9444509	0.91[CHB][hapmap]
rs9450659	0.89[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9450663	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450664	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450665	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450666	0.92[ASN][1000 genomes]
rs9450667	0.80[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9450673	0.85[AMR][1000 genomes]
rs9450677	0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes]
rs9450681	0.91[CHB][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap]
rs9450686	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs9450693	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs9450694	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs9450697	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs9450698	0.91[CHB][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes]
rs9450699	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs9450700	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs9450708	0.91[CHB][hapmap]
rs9450709	0.91[CHB][hapmap]
rs9450716	0.91[CHB][hapmap]
rs9450717	0.91[CHB][hapmap]
rs9450740	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9450661	C6orf162	cis	parietal	SCAN
rs9450661	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs9450661	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs9450661	SLC35A1	cis	parietal	SCAN
rs9450661	C6orf163	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88040600-88116800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:88054800-88110200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:88061600-88094600	Weak transcription	Left Ventricle	heart
4	chr6:88080200-88093800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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